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Commit Graph

7742 Commits

Author SHA1 Message Date
Ward Fisher
379681ff55 Merge branch 'patch-47' of https://github.com/gsjaardema/netcdf-c into 4.8.0-wellspring.wif 2021-03-22 11:48:10 -06:00
Greg Sjaardema
7732ef1c88
Fix if statement to apply to fflush
Even though the `fflush()` is on the same line as the `fprintf(stderr, ...` statement, it is not part of the `if` and is therefore, executed even if the `wdebug` is not active.  This results in `fflush()` being called more than it should.  

Added parenthesis to property protect the fflush call.
2021-03-18 13:49:07 -06:00
Ward Fisher
a9ba3c53b1
Merge pull request from ibaned/cmake-have-mpi-info
HAVE_MPI_INFO_F2C was missing from CMake config.h
2021-03-17 16:14:26 -06:00
Ward Fisher
7de6da8fee Address a C99 forward-declaration issue. 2021-03-17 11:21:23 -06:00
Ward Fisher
34e63705a6 Restored cleanup stanza in tst_filter.sh 2021-03-17 10:34:37 -06:00
Ward Fisher
3b4c04d87f Merge branch 'master' into 3.8.0-wellspring.wif 2021-03-16 10:42:11 -06:00
Dan Ibanez
455fa214d2 HAVE_MPI_INFO_F2C was missing from CMake config.h 2021-03-12 12:33:05 -07:00
Ward Fisher
ca4d0fa087
Merge pull request from bartoldeman/master
Add HAVE_MPI_INFO_F2C to cmake config.h input file
2021-03-11 16:38:41 -07:00
Ward Fisher
ec069646b8 Merge branch '4.8.0-wellspring.wif' of github.com:Unidata/netcdf-c into 4.8.0-wellspring.wif 2021-03-09 13:40:23 -07:00
Ward Fisher
6b2f25818f Fix tst_filter.sh such that it returns an error immediately on failure. 2021-03-09 13:40:12 -07:00
Ward Fisher
2a02e5a32b More modification in support of 2021-03-09 10:49:30 -07:00
Ward Fisher
c5d2937889 Correct bash test failure on Windows in MSYS2 bash shell with Visual Studio-based build, in support of https://github.com/Unidata/netcdf-c/issues/1940 2021-03-08 15:10:50 -07:00
Ward Fisher
c31d5ac655
Merge pull request from DennisHeimbigner/pathmgmt.dmh
Codify cross-platform file paths
2021-03-08 11:23:14 -07:00
Dennis Heimbigner
471268f632 Update RELEASE_NOTES 2021-03-04 13:45:44 -07:00
Dennis Heimbigner
0b7a5382e7 Codify cross-platform file paths
The netcdf-c code has to deal with a variety of platforms:
Windows, OSX, Linux, Cygwin, MSYS, etc.  These platforms differ
significantly in the kind of file paths that they accept.  So in
order to handle this, I have created a set of replacements for
the most common file system operations such as _open_ or _fopen_
or _access_ to manage the file path differences correctly.

A more limited version of this idea was already implemented via
the ncwinpath.h and dwinpath.c code. So this can be viewed as a
replacement for that code. And in path in many cases, the only
change that was required was to replace '#include <ncwinpath.h>'
with '#include <ncpathmgt.h>' and then replace file operation
calls with the NCxxx equivalent from ncpathmgr.h Note that
recently, the ncwinpath.h was renamed ncpathmgmt.h, so this pull
request should not require dealing with winpath.

The heart of the change is include/ncpathmgmt.h, which provides
alternate operations such as NCfopen or NCaccess and which properly
parse and rebuild path arguments to work for the platform on which
the code is executing. This mostly matters for Windows because of the
way that it uses backslash and drive letters, as compared to *nix*.
One important feature is that the user can do string manipulations
on a file path without having to worry too much about the platform
because the path management code will properly handle most mixed cases.
So one can for example concatenate a path suffix that uses forward
slashes to a Windows path and have it work correctly.

The conversion code is in libdispatch/dpathmgr.c, and the
important function there is NCpathcvt which does the proper
conversions to the local path format.

As a rule, most code should just replace their file operations with
the corresponding NCxxx ones defined in include/ncpathmgmt.h. These
NCxxx functions all call NCpathcvt on their path arguments before
executing the actual file operation.

In some rare cases, the client may need to directly use NCpathcvt,
but this should be avoided as much as possible. If there is a need
for supporting a new file operation not already in ncpathmgmt.h, then
use the code in dpathmgr.c as a template. Also please notify Unidata
so we can include it as a formal part or our supported operations.
Also, if you see an operation in the library that is not using the
NCxxx form, then please submit an issue so we can fix it.

Misc. Changes:
* Clean up the utf8 testing code; it is impossible to get some
  tests to work under windows using shell scripts; the args do
  not pass as utf8 but as some other encoding.
* Added an extra utf8 test case: test_unicode_path.sh
* Add a true test for HDF5 1.10.6 or later because as noted in
  PR https://github.com/Unidata/netcdf-c/pull/1794,
  HDF5 changed its Windows file path handling.
2021-03-04 13:41:31 -07:00
Bart Oldeman
0eb1f83fd1 Add HAVE_MPI_INFO_F2C to cmake config.h input file
Without this define parallel netCDF-Fortran did not work
correctly with Open MPI, for example
examples/F90/simple_xy_par_wr.f90
reported
*** An error occurred in MPI_Info_dup
*** reported by process [2543714305,2]
*** on communicator MPI_COMM_WORLD
*** MPI_ERR_INFO: invalid info object
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
***    and potentially your MPI job)

Fixes 
2021-03-04 00:33:20 +00:00
Ward Fisher
f388bcec15
Merge pull request from wsmigaj/bugfix/HDF5_C_LIBRARY_hdf5
Fix name of the HDF5_C_LIBRARY_hdf5 CMake variable
2021-03-02 11:45:59 -07:00
Wojciech Śmigaj
e9ef96b733
Fix name of the HDF5_C_LIBRARY_hdf5 CMake variable 2021-03-02 16:27:19 +00:00
Ward Fisher
e9a7963527
Merge pull request from DennisHeimbigner/memleak.dmh
Fix memory leak in nccopy.c
2021-03-01 10:07:57 -07:00
Ward Fisher
ac332131e7
Merge pull request from lesserwhirls/links
Update links related to netCDF-Java and the TDS
2021-02-26 16:16:10 -07:00
Sean Arms
cd91418dca Update d4ts.war and dts.war build instructions
Caught this one by accident as I was looking for links that needed to be
updated. Figured I might as well knock it out while I was there.
2021-02-26 15:14:57 -07:00
Sean Arms
aefadcc6a5 Update links
Update links to netCDF-java and TDS documentation, as well as
various netCDF related issue trackers.
2021-02-26 15:14:37 -07:00
Sean Arms
e603c10964 Update links to netCDF-java documentation. 2021-02-26 15:11:10 -07:00
Dennis Heimbigner
467faeaaeb Fix memory leak in nccopy.c 2021-02-25 15:06:39 -07:00
Ward Fisher
f18381180c Update number of threads used in doxygen developer config file. 2021-02-25 14:26:57 -07:00
Ward Fisher
d136d46d22
Merge pull request from DennisHeimbigner/deflate.dmh
More fixes to the nccopy filter x chunking algorithm
2021-02-08 11:15:15 -06:00
Ward Fisher
0b6f5c7a27
Merge branch 'master' into deflate.dmh 2021-02-08 11:10:06 -06:00
Ward Fisher
c88dd0580b
Merge pull request from DennisHeimbigner/nczarr_zip.dmh
Add zip file support to nczarr
2021-02-08 11:09:27 -06:00
Ward Fisher
b820b26abd
Merge pull request from brtnfld/master
fixed H5O_info_t incompatiblity with H5Oget_info_by_idx3
2021-02-04 16:35:55 -06:00
Scot Breitenfeld
b34e073f57 Merge remote-tracking branch 'upstream/master' 2021-02-04 11:47:00 -06:00
Dennis Heimbigner
278f19e52d Update RELEASE_NOTES 2021-02-03 11:22:42 -07:00
Dennis Heimbigner
7272ed6ca1 Update RELEASE_NOTES 2021-02-03 11:20:10 -07:00
Dennis Heimbigner
1d9727c616 More fixes to the nccopy filter x chunking algorithm
re: Issue https://github.com/Unidata/netcdf-c/issues/1936

The algorithm controlling interaction of -d 0 -F and -c / options
is incorrect.

The fix:
1. make -d 0 => no deflation
2. make -F properly use the filter specs to decide.

Also added a test case to ncdump/tst_nccopy4.sh.
2021-01-31 15:10:39 -07:00
Dennis Heimbigner
4ae71d3d73 appveyor fix 2021-01-28 20:31:16 -07:00
Dennis Heimbigner
e7d5f24078 Add zip file support
The primary change is to support the use of a zip file as a
storage format. Simultaneously the .nz4 support is made obsolete

Use of zip requires the libzip support library, so a number of
changes to the build files (Makefile.am, CMakeLists.txt) are
necessary to locate and incorporate libzip.  The nczarr_tests
tests are also changed to add zip testing.

Other changes:
* Make sure distcheck leaves no files around.
* Add some functions to netcdf_aux to export some functions of libnetcdf.
* Add a new error NC_EFOUND as the complement of NC_EEMPTY.
* Add tracing support to nclog and use it in libnczarr.
* Modify the zmap interface to support the writeonce semantics of zip.
* Create a new s3util.c to support a variety of S3 auxilliary functions.
* EXTERNL'ize a number of functions so they can be used in s3util.
* Add support for the S3 ListObjects CommonPrefixes mechanism
  to improve search.
* Add experimental support for running nczarr X s3 tests against
  the actual Amazon S3 cloud.
2021-01-28 20:11:01 -07:00
Ward Fisher
f23fe5f6d3
Merge pull request from DennisHeimbigner/actionzarr.dmh
Enable nczarr testing in github actions.
2021-01-27 13:51:19 -07:00
Dennis Heimbigner
480f00bc19 disable run_chunkcases 2021-01-27 11:44:53 -07:00
Dennis Heimbigner
911d0a5deb Enable nczarr testing in github actions.
Changes:
1. add "use_nczarr: [ nczarr_off, nczarr_on ]" to matrix
2. add libzip-dev to the apt installs (might need caching).
3. convert deprecated "--enable-netcdf-4" to "--enable-hdf5" (also for cmake)
2021-01-27 11:30:48 -07:00
Ward Fisher
025fb7b6fe
Merge pull request from rkouznetsov/master
Fix for :60 seconds in ncdump
2021-01-26 14:35:30 -07:00
Ward Fisher
793d2d8c15
Merge pull request from DennisHeimbigner/dap4fixes.dmh
Improve operation of the DAP4 code and fix bugs
2021-01-26 12:30:30 -07:00
Ward Fisher
8f908db1f3
Merge pull request from DennisHeimbigner/dap4retest.dmh
Enable selected DAP tests previously disabled.
2021-01-26 12:30:00 -07:00
Ward Fisher
5afe43639a
Merge pull request from avalentino/fix-hdf5-zlib-check
Fix HDF5_ZLIB check
2021-01-26 11:48:02 -07:00
Ward Fisher
52011297f3
Merge branch 'master' into fix-hdf5-zlib-check 2021-01-26 11:47:52 -07:00
Ward Fisher
8db5519472
Merge branch 'master' into dap4retest.dmh 2021-01-26 11:46:12 -07:00
Rostislav Kouznetsov
74ef4eaa8c Fix for :60 seconds in ncdump
Ncdump reports times like "2015-03-12 12:19:60.000000" 
Imposes a microsecond accuracy on dumped time representation
2021-01-26 10:24:43 +02:00
Ward Fisher
7630f466a2
Merge pull request from gsjaardema/patch-47
Fix so setting of NC_FORMATX_NC3 in parallel is kept
2021-01-21 14:14:28 -07:00
Ward Fisher
dd6490babd
Merge pull request from ibaned/custom-mpi-includes
Ensure MPI works without a wrapper
2021-01-20 13:37:01 -07:00
Dan Ibanez
9ad3e49371 more missing includes for MPI without wrapper 2021-01-19 10:33:08 -07:00
Dan Ibanez
69182dc438 Ensure MPI header found without wrapper 2021-01-19 09:38:07 -07:00
Dennis Heimbigner
c2e25f7bec Forgot baselinehyrax in the dist 2021-01-14 21:49:34 -07:00